extraction of shapes and counts of transcripts within shape boundaries

chkInclusion.R

library(SpatialData)
library(SpatialData.data)
library(sf)
library(SummarizedExperiment)

if (!exists("mb")) mb  = MouseBrainMERFISH()

make_circles = function(spd, shapetype="cells") {
  cshape = SpatialData::shapes(spd)[[shapetype]]
  df1 = data(cshape) |> as.data.frame()
  hh = df1$geometry |> wk::wk_coords() 
  cents = st_as_sf(hh[,c("x", "y")], coords=c(1,2))
  st_buffer(cents, dist=df1$radius)
}

make_points = function(spd, pointtype="single_molecule") {
  p = SpatialData::points(spd)[[pointtype]]
  tmp = p |> dplyr::select(x,y) |> as.data.frame()
  st_as_sf(tmp, coords=c("x", "y"))
}

p = make_points(mb)
circs = make_circles(mb)

int = st_intersects(p,circs)
hits = sapply(int, length) # how often is a point found within cell

sum(hits)
sum(assay(SpatialData::table(mb)))